Genomic profiling reveals the pivotal role of hrHPV driving copy number and gene expression alterations, including mRNA downregulation of TP53 and RB1 in penile cancer

Funda??o de Amparo ? Pesquisa e ao Desenvolvimento Cient?fico e Tecnol?gico do Maranh?o. Grant Numbers: 00971/17, 01352/16. Federal University of Maranh?o. Postgraduate Program in Health Science. S?o Lu?s, MA, Brazil. Federal University of Maranh?o. Department of Biology. Laboratory of Genetics and Molecular Biology. S?o Lu?s, MA, Brazil. Aldenora Bello Cancer Hospital. S?o Lu?s, MA, Brazil. Aldenora Bello Cancer Hospital. S?o Lu?s, MA, Brazil. Federal University of Maranh?o. Postgraduate Program in Health Science. S?o Lu?s, MA, Brazil / Federal University of Maranh?o. Department of Biology. Laboratory of Genetics and Molecular Biology. S?o Lu?s, MA, Brazil. Federal University of Maranh?o. Public Health Department. S?o Lu?s, MA, Brazil. Federal University of Maranh?o. Department of Pathology. Biology Undergraduate Course. S?o Lu?s, MA, Brazil. Federal University of Maranh?o. Postgraduate Program in Health Science. S?o Lu?s, MA, Brazil. Federal University of Maranh?o. Department of Pathology. Biology Undergraduate Course. S?o Lu?s, MA, Brazil. Federal University of Par?. Oncology Research Center. Bel?m, PA, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecido e citogen?tica. Ananindeua, PA, Brasil. Federal University of Maranh?o. Department of Physiological Sciences. S?o Lu?s, MA, Brazil. Faculdades Pequeno Pr?ncipe. Instituto de Pesquisa Pel? Pequeno Pr?ncipe. Curitiba, PR, Brazil / Georgetown Lombardi Comprehensive Cancer Center. Department of Oncology. Washington, District of Columbia, United States. Federal University of Maranh?o. Department of Biology. Laboratory of Genetics and Molecular Biology. S?o Lu?s, MA, Brazil. The incidence of penile cancer (PeCa) is increasing worldwide, however, the highest rates are reported in underdeveloped countries. The molecular mechanisms that underly the onset and progression of these tumors are still unclear. Therefore, our goal was to determine the genome?wide copy number alterations and the involvement of human papiloma virus (HPV) (TP53 and RB1), inflammatory (COX2 and EGFR), and PI3K/AKT pathway (AKT1, AKT2, EGFR, ERBB3, ERBB4, PIK3CA, and PTEN) associated genes in patients with PeCa from a high incidence region in Brazil (Maranh?o). HPV genotyping was performed by nest?PCR and genome sequencing, copy number alterations (CNAs) by array comparative genomic hybridization and gene copy number status, gene, and protein expression by quantitative polymerase chain reaction, reverse transcriptase?quantitative polymerase chain reaction, and immunohistochemistry, respectively. HPV genotyping revealed one of the highest frequencies of HPV reported in PeCa, affecting 96.4% of the cases. The most common CNAs observed were located at the HPV integration sites, such as 2p12?p11.2 and 14q32.33, where ADAM 6, KIAA0125, LINC00226, LINC00221, and miR7641?2, are mapped. Increased copy number of ERBB3 and EGFR genes were observed in association with COX2 and EGFR overexpression, reinforcing the role of the inflammatory pathway in PeCa, and suggesting anti?EGFR and anti?COX2 inhibitors as promising therapies for PeCa. Additionally, TP53 and RB1 messenger RNA downregulation was observed, suggesting the occurrence of other mechanisms for repression of these oncoproteins, in addition to the canonical HPV/TP53/RB1 signaling pathway. Our data reinforce the role of epigenetic events in abnormal gene expression in HPV?associated carcinomas and suggest the pivotal role of HPV driving CNAs and controlling gene expression in PeCa.